MOLECULAR APPROACHES IN NATURAL RESOURCE CONSERVATION AND MANAGEMENT Recent advances in molecular genetics and genomics have been embraced by many scientists in natural resource conservation. Today, several major conservation and management journals are using the “genetics” editors of this book to deal solely with the influx of manuscripts that employ molecular data. The editors have attempted to synthesize some of the major uses of molecular markers in natural resource management in a book targeted not only at scientists but also at individuals actively making conservation and management decisions. To that end, the text features contributors who are major figures in molecular ecology and evolution – many having published books of their own. The aim is to direct and distill the thoughts of these outstanding scientists by compiling compelling case histories in molecular ecology as they apply to natural resource management. J. Andrew DeWoody is Professor of Genetics and University Faculty Scholar at Purdue University. He earned his MS in genetics at Texas A&M University and his PhD in zoology from Texas Tech University. His recent research in genetics, evolution, and ecology has been funded by organizations including the National Science Foundation, the U.S. Department of Agriculture (USDA) National Research Initiative, the Great Lakes Fishery Trust, and the National Geographic Society. His research is published in more than thirty-five journals, and he has served as Associate Editor for the North American Journal of Fisheries Management, the Journal of Wildlife Management,andGenetica. John W. Bickham is Professor in the Department of Forestry and Natural Resources (FNR) and Director of the Center for the Environment at Purdue University. He received his MS in biology from the University of Dayton and his PhD in zoology from Texas Tech University. He was on the faculty of Texas A&M University’s Department of Wildlife and Fisheries Sciences for thirty years. He has published more than two hundred articles in scientific journals in evolutionary genetics, including comparative cytogenetics, molecular systematics, molecular ecology, and ecotoxicology. Charles H. Michler is the Fred M. van Eck Director of the Hardwood Tree Improvement and Regen- eration Center at Purdue University and Site Director of the National Science Foundation Industry & University Cooperative Research Program’s Center for Advanced Forest Systems. He earned his MS and PhD in horticulture, physiology, and biochemistry from The Ohio State University. He has published more than eighty-five scholarly works and has edited nine books and proceedings. He is Editor of Plant Breeding Reviews and Associate Editor of the Journal of Forest Research. Krista M. Nichols is Assistant Professor, Departments of Biological Sciences and Forestry and Natural Resources at Purdue University. She received her MS in fisheries and wildlife from Michigan State University and her PhD in zoology from Washington State University. She was a National Research Council postdoctoral Fellow at the National Marine Fisheries Services, Northwest Fisheries Science Center. Dr. Nichols has published in the fields of ecotoxicology, genetics, and ecology. Olin E. Rhodes, Jr., is Professor in the FNR and Director of the Interdisciplinary Center for Ecological Sustainability at Purdue University. He received his MS in wildlife biology from Clemson University and his PhD in wildlife ecology from Texas Tech University. He was named a Purdue University Faculty Scholar in 2006. He has published more than 135 scholarly works in ecology and genetics and has recently served as Associate Editor of the Journal of Wildlife Management. Keith E. Woeste is a research molecular geneticist for the USDA Forest Service Northern Research Station Hardwood Tree Improvement and Regeneration Center and Adjunct Assistant Professor at Purdue University’s FNR. He received an MDiv in theology from the Jesuit School of Theology at Berkeley, an MS in horticulture from the University of California–Davis, and his PhD in genetics from the University of California–Davis. Molecular Approaches in Natural Resource Conservation and Management Edited by J. Andrew DeWoody Purdue University John W. Bickham Purdue University Charles H. Michler Purdue University Krista M. Nichols Purdue University Olin E. Rhodes, Jr. Purdue University Keith E. Woeste Purdue University CAMBRIDGE UNIVERSITY PRESS Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, Sao˜ Paulo, Delhi, Dubai, Tokyo, Mexico City Cambridge University Press 32 Avenue of the Americas, New York, NY 10013-2473, USA www.cambridge.org Information on this title: www.cambridge.org/9780521731348 C Cambridge University Press 2010 This publication is in copyright. Subject to statutory exception and to the provisions of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. First published 2010 Printed in the United States of America A catalog record for this publication is available from the British Library. Library of Congress Cataloging in Publication data Molecular approaches in natural resource conservation and management / edited by J. Andrew DeWoody . [et al.]. p. cm. Includes bibliographical references and index. ISBN 978-0-521-51564-1 (hardback) – ISBN 978-0-521-73134-8 (pbk.) 1. Biodiversity conservation. 2. Genetic resources conservation. 3. Molecular genetics. 4. Conservation of natural resources. I. DeWoody, J. Andrew, 1969– II. Title. QH75.M647 2010 333.9516–dc22 2009050318 ISBN 978-0-521-51564-1 Hardback ISBN 978-0-521-73134-8 Paperback Cambridge University Press has no responsibility for the persistence or accuracy of URLs for external or third-party Internet Web sites referred to in this publication and does not guarantee that any content on such Web sites is, or will remain, accurate or appropriate. Contents Contributors page ix Preface xv 1 Biodiversity discovery and its importance to conservation 1 Rodney L. Honeycutt, David M. Hillis, and John W. Bickham Box 1: Genetic identification of cryptic species: An example in Rhogeessa 22 Amy B. Baird 2 Gene flow, biodiversity, and genetically modified crops: Weedy rice in Thailand 35 Barbara Schaal, Wesley J. Leverich, Sansanee Jamjod, Chanya Maneechote, Anbreen Bashir, Amena Prommin, Adirek Punyalue, Athitya Suta, Theerasak Sintukhiew, Anupong Wongtamee, Tonapha Pusadee, Sunisa Niruntrayakul, and Benjavan Rerkasem Box 2: Environmental risk assessment of genetically engineered salmon 37 Robert H. Devlin and Fredrik L. Sundstrom¨ 3 A community and ecosystem genetics approach to conservation biology and management 50 Thomas G. Whitham, Catherine A. Gehring, Luke M. Evans, Carri J. LeRoy, Randy K. Bangert, Jennifer A. Schweitzer, Gerard J. Allan, Robert C. Barbour, Dylan G. Fischer, Bradley M. Potts, and Joseph K. Bailey Box 3: Landscape genetics of an American chestnut borer 63 Jeffrey D. Holland 4 Vertebrate sex-determining genes and their potential utility in conservation, with particular emphasis on fishes 74 J. Andrew DeWoody, Matthew C. Hale, and John C. Avise Box 4: Sex identification and population size of grizzly bears by using noninvasive genetic sampling 76 Lisette Waits 5 Historical and contemporary dynamics of adaptive differentiation in European oaks 101 Antoine Kremer, Valerie´ Le Corre, Remy´ J. Petit, and Alexis Ducousso v vi Contents Box 5: Adaptive shifts in natural populations of high dispersing species 117 Stephen R. Palumbi 6 Association genetics, population genomics, and conservation: Revealing the genes underlying adaptation in natural populations of plants and animals 123 Krista M. Nichols and David B. Neale Box 6: Unraveling counterintuitive evolutionary trends: Coat color in Soay sheep 139 Jake Gratten, Alastair J. Wilson, Allan F. McRae, Dario Beraldi, Peter M. Visscher, Josephine M. Pemberton, and Jon Slate 7 Hybridization in threatened and endangered animal taxa: Implications for conservation and management of biodiversity 169 Kelly R. Zamudio and Richard G. Harrison Box 7: Mating opportunities in animal hybrid zones 171 Marjorie Matocq 8 Pollen and seed movement in disturbed tropical landscapes 190 J. L. Hamrick Box 8–1: Effective population size 192 J. L. Hamrick Box 8–2: Allelic recharge in populations recovering from bottleneck events 194 Joseph D. Busch, Jennifer McCreight, and Peter M. Waser 9 Implications of landscape alteration for the conservation of genetic diversity of endangered species 212 Paul L. Leberg, Giridhar N. R. Athrey, Kelly R. Barr, Denise L. Lindsay, and Richard F. Lance Box 9: Dune restoration introduces genetically distinct American beachgrass, Ammophila breviligulata, into a threatened local population 214 Julie R. Etterson and Rebecca M. Holmstrom 10 Integrating evolutionary considerations into recovery planning for Pacific salmon 239 Robin S. Waples, Michelle M. McClure, Thomas C. Wainwright, Paul McElhany, and Peter W. Lawson Box 10: The Kermode bear: A swirl of scientific, management, and ethical values in British Columbia 259 Kermit Ritland 11 Using molecular methods to improve the genetic management of captive breeding programs for threatened species 267 Jamie A. Ivy and Robert C. Lacy Box 11: Pedigree reconstruction: An alternative to systematic breeding 285 Yousry A. El-Kassaby Contents vii 12 Wildlife reintroductions: The conceptual development and application of theory 296 Olin E. Rhodes, Jr., and Emily K. Latch Box 12: Genetic ramifications of restoration of blight-resistant American